Multiple myeloma–associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress Liang Chu, … , Ravi Vij, Michael H. Tomasson J Clin Invest. 2012;122(8):2793-2806. https://doi.org/10.1172/JCI63051. Research Article The histone methyltransferase WHSC1 (also known as MMSET) is overexpressed in multiple myeloma (MM) as a result of the t(4;14) chromosomal translocation and in a broad variety of other cancers by unclear mechanisms. Overexpression of WHSC1 did not transform wild-type or tumor-prone primary hematopoietic cells. We found that ACA11, an orphan box H/ACA class small nucleolar RNA (snoRNA) encoded within an intron of WHSC1, was highly expressed in t(4;14)-positive MM and other cancers. ACA11 localized to nucleoli and bound what we believe to be a novel small nuclear ribonucleoprotein (snRNP) complex composed of several proteins involved in postsplicing intron complexes. RNA targets of this uncharacterized snRNP included snoRNA intermediates hosted within ribosomal protein (RP) genes, and an RP gene signature was strongly associated with t(4;14) in patients with MM. Expression of ACA11 was sufficient to downregulate RP genes and other snoRNAs implicated in the control of oxidative stress. ACA11 suppressed oxidative stress, afforded resistance to chemotherapy, and increased the proliferation of MM cells, demonstrating that ACA11 is a critical target of the t(4;14) translocation in MM and suggesting an oncogenic role in other cancers as well. Find the latest version: https://jci.me/63051/pdf Related Commentary, page 2765 Research article Multiple myeloma–associated chromosomal translocation activates orphan snoRNA ACA11 to suppress oxidative stress Liang Chu,1 Mack Y. Su,1 Leonard B. Maggi Jr.,1 Lan Lu,1 Chelsea Mullins,1 Seth Crosby,2 Gaofeng Huang,3 Wee Joo Chng,3,4,5,6 Ravi Vij,1 and Michael H. Tomasson1,2 1Division of Oncology and 2Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. 3Yong Loo Lin School of Medicine, 4Department of Haematology-Oncology, National University Cancer Institute of Singapore, 5National University Health System, and 6Cancer Science Institute of Singapore, National University of Singapore, Singapore. The histone methyltransferase WHSC1 (also known as MMSET) is overexpressed in multiple myeloma (MM) as a result of the t(4;14) chromosomal translocation and in a broad variety of other cancers by unclear mecha- nisms. Overexpression of WHSC1 did not transform wild-type or tumor-prone primary hematopoietic cells. We found that ACA11, an orphan box H/ACA class small nucleolar RNA (snoRNA) encoded within an intron of WHSC1, was highly expressed in t(4;14)-positive MM and other cancers. ACA11 localized to nucleoli and bound what we believe to be a novel small nuclear ribonucleoprotein (snRNP) complex composed of sev- eral proteins involved in postsplicing intron complexes. RNA targets of this uncharacterized snRNP included snoRNA intermediates hosted within ribosomal protein (RP) genes, and an RP gene signature was strongly associated with t(4;14) in patients with MM. Expression of ACA11 was sufficient to downregulate RP genes and other snoRNAs implicated in the control of oxidative stress. ACA11 suppressed oxidative stress, afforded resistance to chemotherapy, and increased the proliferation of MM cells, demonstrating that ACA11 is a criti- cal target of the t(4;14) translocation in MM and suggesting an oncogenic role in other cancers as well. Introduction fied for WHSC1 (18, 19). Third, WHSC1 knockdown using shRNAs Multiple myeloma (MM) is an incurable cancer of B-lineage plasma decreases cell growth and cell adhesion in MM and neuroblasto- cells, associated with anemia, renal failure, and cortical bone destruc- ma cell lines (8, 10, 15, 20). Knockdown using a variety of shRNA tion (1). The recurrent t(4;14)(p16.3;q32.3) chromosomal transloca- constructs has established the dependence of transformed cells on tion is detected in 20% of MMs and is associated with shortened WHSC1 expression, but which WHSC1 isoform is responsible for overall survival (2–5). The t(4;14) transposes immunoglobulin heavy cell transformation has not been clearly established. chain region enhancer elements to the 5′ end of the Wolf-Hirschhorn A difficult-to-explain clue into the cell biology of WHSC1 is syndrome candidate 1 gene (WHSC1; also known as MMSET and that a subset of t(4;14) patients with MM harbor translocation NSD2) to drive its ectopic expression (4, 6). WHSC1 encodes 3 breakpoints that result in the overexpression of amino-truncated protein isoforms that are expressed as a result of alternative splic- WHSC1 proteins. Loss of a nucleolar exclusion signal at the amino ing (WHSC1-I and WHSC1-II) and an internal promoter (REIIBP; terminus of WHSC1-II causes altered subcellular localization of refs. 6, 7, and Supplemental Figure 1A; supplemental material available these shortened WHSC1 protein products (21), and Ser102 is lost in online with this article; doi:10.1172/JCI63051DS1). The WHSC1-II these truncations, affecting function of WHSC1 in DNA repair (9). and REIIBP isoforms contain a SET domain that encodes a histone Yet, the clinical course of t(4;14)-positive patients is independent of methyltransferase (HMT), with activity reported toward H4K20 (8, 9), the location of the translocation breakpoints within WHSC1 (21). H3K36 (10, 11), and H3K27 (12). The HMT activity of WHSC1-II Therefore, the precise mechanism by which these different WHSC1 plays a role in DNA damage responses by recruiting repair factors to gene products contribute to transformation remains unclear. DNA breaks, and this recruitment is dependent upon phosphoryla- To improve our understanding of how the t(4;14) contributes to tion of WHSC1-II Ser102 by ATM (9, 13). myelomagenesis, we evaluated the effects of 3 major WHSC1 isoforms Three lines of evidence support the role of WHSC1 as an onco- (WHSC1-I, WHSC1-II, and REIIBP) on hematopoietic cell trans- gene. First, WHSC1 transcripts are consistently overexpressed in formation. Despite an extensive set of reverse genetic experiments, t(4;14)-positive myelomas, and WHSC1 is also upregulated by none of the WHSC1 proteins demonstrated significant pro-growth unknown mechanisms in subsets of diverse solid tumor types, effects. These unexpected results prompted us to examine the 4p16.3 including neuroblastoma, in which high WHSC1 levels are associ- breakpoint region in t(4;14)-positive patients with MM for a missing ated with tumor aggressiveness (14–16). Second, transcriptional oncogene. Using RNA tiling arrays, we identified what we believe to deregulation by the HMT encoded by WHSC1 is a plausible mech- be a novel box H/ACA ncRNA, ACA11, encoded within intron 18–19 anism of carcinogenesis. Indeed, H3K36 methyltransferase activity of the WHSC1 gene overexpressed in t(4;14)-positive MM and other can be sufficient to initiate malignant transformation (17), and cancers. ACA11 is an orphan small nucleolar RNA (snoRNA) that attractive candidate target genes and pathways have been identi- binds what we believe to be a novel small nuclear ribonucleoprotein (snRNP) complex in MM cells. Overexpression of ACA11 protected Conflict of interest: The authors have declared that no conflict of interest exists. MM cells from oxidative stress and modulated tumor proliferation, Citation for this article: J Clin Invest. 2012;122(8):2793–2806. doi:10.1172/JCI63051. and knockdown of ACA11 slowed cell proliferation and sensitized The Journal of Clinical Investigation http://www.jci.org Volume 122 Number 8 August 2012 2793 research article 2794 The Journal of Clinical Investigation http://www.jci.org Volume 122 Number 8 August 2012 research article Figure 1 WHSC1 exon sequences, 1 substantial segment mapped to ACA11 ACA11 is activated by t(4;14) in MM. (A) Schematic diagram of the (SCARNA22), a 125-bp noncoding RNA (ncRNA) located within chromosome 4p16.3 tiling oligonucleotide microarray, spanning 430 Kb intron 18–19 of WHSC1 (Figure 1, B and C, and Supplemental across the t(4;14) breakpoint region (breakpoints are indicated by Figure 3, A and B). Robust expression of ACA11 was significant- arrows). Annotated genes are indicated with exon structures. (B) Til- ing microarray expression data of representative t(4;14)-positive and ly associated with the t(4;14) translocation in MM cell lines and -negative patients with MM. (C) Heat map of t(4;14)-positive (Y; n = 4) patient samples (Figure 1, D–F). ACA11 was also overexpressed in and -negative (N; n = 12) patient samples. (B and C) Numbers indicate a subset of samples from patients with primary colon, esophageal, base pairs on chromosome 4 (human genome assembly GRCh37). and bladder cancer (Figure 2), consistent with its location within (D) Real-time PCR of ACA11 in samples from patients with MM. The WHSC1 (16). These data confirm ACA11 overexpression in t(4;14)- inset shows that ACA11 is significantly associated with t(4;14) status. positive MM, but additional studies are required to confirm the + Normal, normal plasma cells (n = 10); t(4;14) , t(4;14)-positive patient hypothesis that ACA11 is upregulated in other cancer types. samples (n = 6); t(4;14)–, t(4;14)-negative patient samples (n = 57). (E) ACA11 is a box H/ACA snoRNA. The predicted secondary structure Northern blot of ACA11 expression in human MM cell lines. t(4;14)-pos- itive cell lines included KMS-11, OPM-2, LP-1, and H929 cells; t(4;14)- of ACA11 was typical of box H/ACA ncRNAs and revealed 2 hair- negative cell lines included U266, RPMI8226, and MM.1S cells; and pin elements connected by a single-stranded hinge carrying the non-MM cell lines included K562, HeLa, A375, and U1A cells. Loading canonical H box (AnAnnA) followed by a 3′ tail containing the ACA controls were 28S and 18S rRNA. (F) ACA11 expression by real-time box (Figure 3A).